Name | Description | Type | Package | Framework |
ABINITFormat | | Class | org.openscience.cdk.io.formats | CDK |
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Aces2Format | | Class | org.openscience.cdk.io.formats | CDK |
|
ADFFormat | | Class | org.openscience.cdk.io.formats | CDK |
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AlchemyFormat | | Class | org.openscience.cdk.io.formats | CDK |
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BGFFormat | | Class | org.openscience.cdk.io.formats | CDK |
|
BooleanIOSetting | An class for a reader setting which must be of type String. | Class | org.openscience.cdk.io.setting | CDK |
|
BSFormat | | Class | org.openscience.cdk.io.formats | CDK |
|
CacaoCartesianFormat | | Class | org.openscience.cdk.io.formats | CDK |
|
CacaoInternalFormat | | Class | org.openscience.cdk.io.formats | CDK |
|
CACheFormat | | Class | org.openscience.cdk.io.formats | CDK |
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CDKConvention | This is an implementation for the CDK convention. | Class | org.openscience.cdk.io.cml | CDK |
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CDKOWLFormat | Serializes a CDK model into the Web Ontology Language using theBelongs to the set:io-formats | Class | org.openscience.cdk.io.formats | CDK |
|
CDKOWLReader | Reads content from a CDK OWL serialization. | Class | org.openscience.cdk.io.rdf | CDK |
|
CDKOWLWriter | Serializes the data model into CDK OWL. | Class | org.openscience.cdk.io.rdf | CDK |
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CDKSourceCodeFormat | | Class | org.openscience.cdk.io.formats | CDK |
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CDKSourceCodeWriter | Converts a Molecule into CDK source code that would build the same molecule. | Class | org.openscience.cdk.io | CDK |
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Chem3D_Cartesian_1Format | | Class | org.openscience.cdk.io.formats | CDK |
|
Chem3D_Cartesian_2Format | | Class | org.openscience.cdk.io.formats | CDK |
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ChemDrawFormat | | Class | org.openscience.cdk.io.formats | CDK |
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ChemtoolFormat | | Class | org.openscience.cdk.io.formats | CDK |
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CIFFormat | | Class | org.openscience.cdk.io.formats | CDK |
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CIFReader | This is not a reader for the CIF and mmCIF crystallographic formats. | Class | org.openscience.cdk.io | CDK |
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CMLCoreModule | Core CML 1. | Class | org.openscience.cdk.io.cml | CDK |
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CMLErrorHandler | CDK's SAX2 ErrorHandler for giving feedback on XML errors in the CML document. | Class | org.openscience.cdk.io.cml | CDK |
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CMLFormat | | Class | org.openscience.cdk.io.formats | CDK |
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CMLHandler | SAX2 implementation for CML XML fragment reading. | Class | org.openscience.cdk.io.cml | CDK |
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CMLReactionModule | | Class | org.openscience.cdk.io.cml | CDK |
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CMLReader | Reads a molecule in CML 1. | Class | org.openscience.cdk.io | CDK |
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CMLResolver | This class resolves DOCTYPE declaration for Chemical Markup Language (CML) files and uses a local version for validation. | Class | org.openscience.cdk.io.cml | CDK |
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CMLRSSFormat | | Class | org.openscience.cdk.io.formats | CDK |
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CMLStack | Low weigth alternative to Sun's Stack class. | Class | org.openscience.cdk.io.cml | CDK |
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CMLWriter | Serializes a IMoleculeSet or a IMolecule object to CML 2 code. | Class | org.openscience.cdk.io | CDK |
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CRK2DFormat | | Class | org.openscience.cdk.io.formats | CDK |
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CRK3DFormat | | Class | org.openscience.cdk.io.formats | CDK |
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CrystClustFormat | | Class | org.openscience.cdk.io.formats | CDK |
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CrystClustReader | | Class | org.openscience.cdk.io | CDK |
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CrystClustWriter | Rather stupid file format used for storing crystal information. | Class | org.openscience.cdk.io | CDK |
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CTXFormat | | Class | org.openscience.cdk.io.formats | CDK |
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CTXReader | Reader that extracts information from the IDENT, NAME, ATOMS and BONDS blocks in CTX files. | Class | org.openscience.cdk.io | CDK |
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CustomSerializer | Custom Serializer with the sole purpose and functionality to not output the XML declaration. | Class | org.openscience.cdk.io.cml | CDK |
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DaltonFormat | | Class | org.openscience.cdk.io.formats | CDK |
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DefaultChemObjectReader | Abstract class that ChemObjectReader's can implement to have it take care of basic stuff, like managing the ReaderListeners. | Class | org.openscience.cdk.io | CDK |
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DefaultChemObjectWriter | Abstract class that ChemObjectReader's can implement to have it take care of basic stuff, like managing the ReaderListeners. | Class | org.openscience.cdk.io | CDK |
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DefaultEventChemObjectReader | Abstract class that IteratingChemObjectReader's can implement to have it take care of basic stuff, like managing the ReaderListeners. | Class | org.openscience.cdk.io.iterator.event | CDK |
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DefaultIteratingChemObjectReader | Abstract class that IteratingChemObjectReader's can implement to have it take care of basic stuff, like managing the ReaderListeners. | Class | org.openscience.cdk.io.iterator | CDK |
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DefaultRandomAccessChemObjectReader | Abstract class that IRandomAccessChemObjectReader's can implement to have it take care of basic stuff, like managing the ReaderListeners. | Class | org.openscience.cdk.io.random | CDK |
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DMol3Format | | Class | org.openscience.cdk.io.formats | CDK |
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DOCK5Format | | Class | org.openscience.cdk.io.formats | CDK |
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EventCMLHandler | CDO object needed as interface with the JCFL library for reading CML in a event based manner. | Class | org.openscience.cdk.io.iterator.event | CDK |
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EventCMLReader | Reads a molecule in CML 1. | Class | org.openscience.cdk.io.iterator.event | CDK |
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FenskeHall_ZMatrixFormat | | Class | org.openscience.cdk.io.formats | CDK |
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FingerprintFormat | | Class | org.openscience.cdk.io.formats | CDK |
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FormatFactory | A factory for recognizing chemical file formats. | Class | org.openscience.cdk.io | CDK |
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GamessFormat | | Class | org.openscience.cdk.io.formats | CDK |
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GamessReader | A reader for GAMESS log file. | Class | org.openscience.cdk.io | CDK |
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Gaussian03Format | | Class | org.openscience.cdk.io.formats | CDK |
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Gaussian03Reader | A reader for Gaussian03 output. | Class | org.openscience.cdk.io | CDK |
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Gaussian90Format | | Class | org.openscience.cdk.io.formats | CDK |
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Gaussian92Format | | Class | org.openscience.cdk.io.formats | CDK |
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Gaussian94Format | | Class | org.openscience.cdk.io.formats | CDK |
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Gaussian95Format | | Class | org.openscience.cdk.io.formats | CDK |
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Gaussian98Format | | Class | org.openscience.cdk.io.formats | CDK |
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Gaussian98Reader | A reader for Gaussian98 output. | Class | org.openscience.cdk.io | CDK |
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GaussianInputFormat | | Class | org.openscience.cdk.io.formats | CDK |
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GaussianInputWriter | File writer thats generates input files for Gaussian calculation jobs. | Class | org.openscience.cdk.io.program | CDK |
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GhemicalMMFormat | | Class | org.openscience.cdk.io.formats | CDK |
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GhemicalMMReader | http://www. | Class | org.openscience.cdk.io | CDK |
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GhemicalSPMFormat | | Class | org.openscience.cdk.io.formats | CDK |
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GROMOS96Format | | Class | org.openscience.cdk.io.formats | CDK |
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HINFormat | | Class | org.openscience.cdk.io.formats | CDK |
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HINReader | Reads an object from HIN formated input. | Class | org.openscience.cdk.io | CDK |
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HINWriter | Writer that outputs in the HIN format. | Class | org.openscience.cdk.io | CDK |
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IChemFormat | This class is the interface that all ChemFormat's should implement. | Interface | org.openscience.cdk.io.formats | CDK |
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IChemFormatMatcher | This interface is used for classes that are able to match a certain chemical file format. | Interface | org.openscience.cdk.io.formats | CDK |
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IChemObjectIO | This class is the interface that all IO readers should implement. | Interface | org.openscience.cdk.io | CDK |
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IChemObjectIOListener | Allows monitoring of progress of file reader activities. | Interface | org.openscience.cdk.io.listener | CDK |
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IChemObjectReader | This interface specifies the common functionality all IO readers should provide. | Interface | org.openscience.cdk.io | CDK |
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IChemObjectReader .Mode | Only fail on serious format problemsFail on any format problem | Class | org.openscience.cdk.io | CDK |
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IChemObjectReaderErrorHandler | Interface for classes aimed to handle IChemObjectReader errors. | Interface | org.openscience.cdk.io | CDK |
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IChemObjectWriter | This class is the interface that all IO writers should implement. | Interface | org.openscience.cdk.io | CDK |
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ICMLConvention | This interface describes the procedures classes must implement to be plugable into the CMLHandler. | Interface | org.openscience.cdk.io.cml | CDK |
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ICMLModule | This interface describes the procedures classes must implement to be plugable into the CMLHandler. | Interface | org.openscience.cdk.io.cml | CDK |
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IEventChemObjectReader | Interface for an iterating molecule reader. | Interface | org.openscience.cdk.io.iterator.event | CDK |
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IIteratingChemObjectReader | Interface for an iterating molecule reader. | Interface | org.openscience.cdk.io.iterator | CDK |
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INChIContentProcessorTool | Tool to help process INChI 1. | Class | org.openscience.cdk.io.inchi | CDK |
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INChIFormat | | Class | org.openscience.cdk.io.formats | CDK |
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INChIHandler | SAX2 implementation for INChI XML fragment parsing. | Class | org.openscience.cdk.io.inchi | CDK |
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INChIPlainTextFormat | | Class | org.openscience.cdk.io.formats | CDK |
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INChIPlainTextReader | Reads the content of a IUPAC/NIST Chemical Identifier (INChI) plain text document. | Class | org.openscience.cdk.io | CDK |
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INChIReader | Reads the content of a IUPAC/NIST Chemical Identifier (INChI) document. | Class | org.openscience.cdk.io | CDK |
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IntegerIOSetting | An class for a reader setting which must be of type String. | Class | org.openscience.cdk.io.setting | CDK |
|
IOSetting | An interface for reader settings. | Class | org.openscience.cdk.io.setting | CDK |
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IRandomAccessChemObjectReader | Extension of ListIterator. | Interface | org.openscience.cdk.io.random | CDK |
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IReaderListener | Allows monitoring of progress of file reader activities. | Interface | org.openscience.cdk.io.listener | CDK |
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IResourceFormat | This class is the interface that all ResourceFormat's should implement. | Interface | org.openscience.cdk.io.formats | CDK |
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ISimpleChemObjectReader | This class is the interface that all IO readers should implement. | Interface | org.openscience.cdk.io | CDK |
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IteratingMDLConformerReader | Iterate over conformers of a collection of molecules stored in SDF format. | Class | org.openscience.cdk.io.iterator | CDK |
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IteratingMDLReader | Iterating MDL SDF reader. | Class | org.openscience.cdk.io.iterator | CDK |
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IteratingPCCompoundASNReader | Iterating PubChem PCCompound ASN reader. | Class | org.openscience.cdk.io.iterator | CDK |
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IteratingPCCompoundXMLReader | Iterating PubChem PCCompound ASN. | Class | org.openscience.cdk.io.iterator | CDK |
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IteratingPCSubstancesXMLReader | Iterating PubChem PC-Substances ASN. | Class | org.openscience.cdk.io.iterator | CDK |
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IteratingSMILESReader | Iterating SMILES file reader. | Class | org.openscience.cdk.io.iterator | CDK |
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IWriterListener | | Interface | org.openscience.cdk.io.listener | CDK |
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JaguarFormat | | Class | org.openscience.cdk.io.formats | CDK |
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JMEFormat | | Class | org.openscience.cdk.io.formats | CDK |
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JMOLANIMATIONConvention | | Class | org.openscience.cdk.io.cml | CDK |
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MacroModelFormat | | Class | org.openscience.cdk.io.formats | CDK |
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MDLFormat | | Class | org.openscience.cdk.io.formats | CDK |
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MDLMolConvention | | Class | org.openscience.cdk.io.cml | CDK |
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MDLReader | Reads a molecule from the original MDL MOL or SDF file . | Class | org.openscience.cdk.io | CDK |
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MDLRXNFormat | | Class | org.openscience.cdk.io.formats | CDK |
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MDLRXNReader | Reads a molecule from an MDL RXN file . | Class | org.openscience.cdk.io | CDK |
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MDLRXNV2000Reader | Reads a molecule from an MDL RXN file . | Class | org.openscience.cdk.io | CDK |
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MDLRXNV3000Format | | Class | org.openscience.cdk.io.formats | CDK |
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MDLRXNV3000Reader | Class that implements the new MDL mol format introduced in August 2002. | Class | org.openscience.cdk.io | CDK |
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MDLRXNWriter | Writes a reaction to a MDL rxn or SDF file. | Class | org.openscience.cdk.io | CDK |
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MDLV2000Format | | Class | org.openscience.cdk.io.formats | CDK |
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MDLV2000Reader | Reads content from MDL molfiles and SD files. | Class | org.openscience.cdk.io | CDK |
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MDLV2000Writer | Writes MDL molfiles, which contains a single molecule (see ). | Class | org.openscience.cdk.io | CDK |
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MDLV3000Format | | Class | org.openscience.cdk.io.formats | CDK |
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MDLV3000Reader | Class that implements the MDL mol V3000 format. | Class | org.openscience.cdk.io | CDK |
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MDMoleculeConvention | | Class | org.openscience.cdk.io.cml | CDK |
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MMODFormat | | Class | org.openscience.cdk.io.formats | CDK |
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Mol2Format | | Class | org.openscience.cdk.io.formats | CDK |
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Mol2Reader | Reads a molecule from an Mol2 file, such as written by Sybyl. | Class | org.openscience.cdk.io | CDK |
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Mol2Writer | An output Writer that writes molecular data into the Tripos Mol2 format. | Class | org.openscience.cdk.io | CDK |
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MOPAC2002Format | | Class | org.openscience.cdk.io.formats | CDK |
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MOPAC7Format | | Class | org.openscience.cdk.io.formats | CDK |
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MOPAC93Format | | Class | org.openscience.cdk.io.formats | CDK |
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MOPAC97Format | | Class | org.openscience.cdk.io.formats | CDK |
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MoSSOutputFormat | | Class | org.openscience.cdk.io.formats | CDK |
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MoSSOutputReader | Reader for MoSS output files which present the results of a substructure mining study. | Class | org.openscience.cdk.io | CDK |
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MPQCFormat | | Class | org.openscience.cdk.io.formats | CDK |
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NWChemFormat | | Class | org.openscience.cdk.io.formats | CDK |
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OptionIOSetting | An class for a reader setting which must be found in the list of possible settings. | Class | org.openscience.cdk.io.setting | CDK |
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PCCompoundASNReader | Reads an object from ASN formated input for PubChem Compound entries. | Class | org.openscience.cdk.io | CDK |
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PCCompoundXMLReader | Reads an object from ASN. | Class | org.openscience.cdk.io | CDK |
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PCModelFormat | | Class | org.openscience.cdk.io.formats | CDK |
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PCSubstanceXMLReader | Reads an object from ASN formated input for PubChem Compound entries. | Class | org.openscience.cdk.io | CDK |
|
PDBConvention | This is a lousy implementation, though. | Class | org.openscience.cdk.io.cml | CDK |
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PDBFormat | | Class | org.openscience.cdk.io.formats | CDK |
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PDBMLFormat | XML version of the PDB format. | Class | org.openscience.cdk.io.formats | CDK |
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PDBReader | Reads the contents of a PDBFile. | Class | org.openscience.cdk.io | CDK |
|
PDBWriter | Saves small molecules in a rudimentary PDB format. | Class | org.openscience.cdk.io | CDK |
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PMPConvention | | Class | org.openscience.cdk.io.cml | CDK |
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PMPFormat | | Class | org.openscience.cdk.io.formats | CDK |
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PMPReader | Reads an frames from a PMP formated input. | Class | org.openscience.cdk.io | CDK |
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POVRayFormat | | Class | org.openscience.cdk.io.formats | CDK |
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PQSChemFormat | | Class | org.openscience.cdk.io.formats | CDK |
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PropertiesListener | Answers the questions by looking up the values in a Properties object. | Class | org.openscience.cdk.io.listener | CDK |
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PubChemASNFormat | | Class | org.openscience.cdk.io.formats | CDK |
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PubChemCompoundsXMLFormat | | Class | org.openscience.cdk.io.formats | CDK |
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PubChemCompoundXMLFormat | | Class | org.openscience.cdk.io.formats | CDK |
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PubChemFormat | | Class | org.openscience.cdk.io.formats | CDK |
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PubChemSubstancesASNFormat | | Class | org.openscience.cdk.io.formats | CDK |
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PubChemSubstancesXMLFormat | | Class | org.openscience.cdk.io.formats | CDK |
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PubChemSubstanceXMLFormat | | Class | org.openscience.cdk.io.formats | CDK |
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PubChemXMLHelper | Helper class to parse PubChem XML documents. | Class | org.openscience.cdk.io.pubchemxml | CDK |
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QChemFormat | | Class | org.openscience.cdk.io.formats | CDK |
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QSARConvention | This is an implementation for the CDK convention. | Class | org.openscience.cdk.io.cml | CDK |
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RandomAccessReader | Random access to text files of compounds. | Class | org.openscience.cdk.io.random | CDK |
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RandomAccessSDFReader | Random access of SDF file. | Class | org.openscience.cdk.io.random | CDK |
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RawCopyFormat | | Class | org.openscience.cdk.io.formats | CDK |
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ReaderEvent | Signals that something has happened in a file reader. | Class | org.openscience.cdk.io | CDK |
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ReaderFactory | A factory for creating ChemObjectReaders. | Class | org.openscience.cdk.io | CDK |
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RGroupQueryFormat | Format for Symyx RGfiles (Rgroup query files). | Class | org.openscience.cdk.io.formats | CDK |
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RGroupQueryReader | A reader for Symyx' Rgroup files (RGFiles). | Class | org.openscience.cdk.io | CDK |
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RGroupQueryWriter | A writer for Symyx' Rgroup files (RGFiles). | Class | org.openscience.cdk.io | CDK |
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RssWriter | Generates an RSS feed. | Class | org.openscience.cdk.io | CDK |
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SDFFormat | | Class | org.openscience.cdk.io.formats | CDK |
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SDFWriter | Writes MDL SD files (). | Class | org.openscience.cdk.io | CDK |
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ShelXFormat | | Class | org.openscience.cdk.io.formats | CDK |
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ShelXReader | A reader for ShelX output (RES) files. | Class | org.openscience.cdk.io | CDK |
|
ShelXWriter | Serializes a MoleculeSet or a Molecule object to ShelX code. | Class | org.openscience.cdk.io | CDK |
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SMARTSFormat | | Class | org.openscience.cdk.io.formats | CDK |
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SMILESFIXFormat | | Class | org.openscience.cdk.io.formats | CDK |
|
SMILESFormat | | Class | org.openscience.cdk.io.formats | CDK |
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SMILESReader | This Reader reads files which has one SMILES string on each line, where the format is given as below: | Class | org.openscience.cdk.io | CDK |
|
SMILESWriter | Writes the SMILES strings to a plain text file. | Class | org.openscience.cdk.io | CDK |
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SpartanFormat | | Class | org.openscience.cdk.io.formats | CDK |
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StringIOSetting | An class for a reader setting which must be of type String. | Class | org.openscience.cdk.io.setting | CDK |
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SVGFormat | | Class | org.openscience.cdk.io.formats | CDK |
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SwingGUIListener | Allows processing of IOSetting quesions which are passed to the user by using Swing dialogs. | Class | org.openscience.cdk.io.listener | CDK |
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SybylDescriptorFormat | | Class | org.openscience.cdk.io.formats | CDK |
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TextGUIListener | Allows processing of IOSetting quesions which are passed to the user by using the System. | Class | org.openscience.cdk.io.listener | CDK |
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TinkerMM2Format | | Class | org.openscience.cdk.io.formats | CDK |
|
TinkerXYZFormat | | Class | org.openscience.cdk.io.formats | CDK |
|
TurboMoleFormat | | Class | org.openscience.cdk.io.formats | CDK |
|
UniChemXYZFormat | | Class | org.openscience.cdk.io.formats | CDK |
|
VASPFormat | | Class | org.openscience.cdk.io.formats | CDK |
|
VASPReader | Read output files generated with the VASP software. | Class | org.openscience.cdk.io | CDK |
|
ViewmolFormat | | Class | org.openscience.cdk.io.formats | CDK |
|
WriterFactory | Helper tool to create IChemObjectWriters. | Class | org.openscience.cdk.io | CDK |
|
XEDFormat | | Class | org.openscience.cdk.io.formats | CDK |
|
XYZFormat | | Class | org.openscience.cdk.io.formats | CDK |
|
XYZReader | Reads an object from XYZ formated input. | Class | org.openscience.cdk.io | CDK |
|
XYZWriter | | Class | org.openscience.cdk.io | CDK |
|
YasaraFormat | | Class | org.openscience.cdk.io.formats | CDK |
|
ZindoFormat | | Class | org.openscience.cdk.io.formats | CDK |
|
ZMatrixFormat | | Class | org.openscience.cdk.io.formats | CDK |
|
ZMatrixReader | It reads Z matrices like in Gaussian input files. | Class | org.openscience.cdk.io | CDK |